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-rw-r--r--libcrystfel/src/index.c14
-rw-r--r--libcrystfel/src/index.h2
-rw-r--r--src/indexamajig.c9
-rw-r--r--src/process_image.c1
4 files changed, 13 insertions, 13 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index c2f79eff..341abf58 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -63,9 +63,9 @@
#include "uthash.h"
-
/** \file index.h */
+
struct _indexingprivate
{
IndexingFlags flags;
@@ -79,6 +79,7 @@ struct _indexingprivate
void **engine_private;
};
+
static const char *onoff(int a)
{
if ( a ) return "on";
@@ -99,6 +100,7 @@ static void set_last_task(char *lt, const char *task)
strcpy(lt, task);
}
+
static void show_indexing_flags(IndexingFlags flags)
{
STATUS("Indexing parameters:\n");
@@ -404,7 +406,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
pinkIndexer_opts,
felix_opts,
ttopts,
- filename);
+ filename);
if ( ipriv->engine_private[i] == NULL ) return NULL;
@@ -639,8 +641,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
case INDEXING_FILE :
set_last_task(last_task, "indexing:file");
- int crystal_number = 0;
- r = fromfile_index(image, mpriv, crystal_number);
+ r = fromfile_index(image, mpriv, 0);
break;
case INDEXING_FELIX :
@@ -942,7 +943,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
int ntry = 0;
int success = 0;
- if ( ipriv->methods[0] != INDEXING_FILE){
+ if ( ipriv->methods[0] != INDEXING_FILE ) {
image->features = sort_peaks(orig);
}
@@ -960,7 +961,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
} while ( !done );
- if ( ipriv->methods[0] != INDEXING_FILE){
+ if ( ipriv->methods[0] != INDEXING_FILE ) {
image_feature_list_free(image->features);
}
@@ -979,6 +980,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
image->indexed_by = INDEXING_NONE;
}
+ image->features = orig;
}
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 92406604..5cee29b2 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -73,7 +73,7 @@ typedef enum {
INDEXING_FELIX = 4, /**< Invoke Felix program */
INDEXING_XDS = 5, /**< Invoke XDS program (NB not nXDS) */
INDEXING_SIMULATION = 6, /**< Dummy value for simulated data */
- INDEXING_FILE = 7, /**< Results injector for debugging */
+ INDEXING_FILE = 7, /**< Results injector for debugging */
INDEXING_ASDF = 8, /**< Use built-in ASDF algorithm */
INDEXING_TAKETWO = 9, /**< Use built-in TakeTwo algorithm */
INDEXING_XGANDALF = 10, /**< Use XGANDALF (via optional library) */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 4b12194c..7f73cef6 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -849,7 +849,6 @@ int main(int argc, char *argv[])
ERROR("Failed to open input file '%s'\n", args.filename);
return 1;
}
-
/* Check prefix (if given) */
if ( args.check_prefix ) {
@@ -997,10 +996,10 @@ int main(int argc, char *argv[])
xgandalf_opts,
pinkindexer_opts,
felix_opts,
- args.filename);
-
- free(args.filename);
-
+ args.filename);
+
+ free(args.filename);
+
if ( args.iargs.ipriv == NULL ) {
ERROR("Failed to set up indexing system\n");
return 1;
diff --git a/src/process_image.c b/src/process_image.c
index d3355f38..825e57d9 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -381,7 +381,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
}
}
-
if ( iargs->fix_profile_r < 0.0 ) {
for ( i=0; i<image->n_crystals; i++ ) {
if ( refine_radius(image->crystals[i], image) ) {